April 1, 2014 (Vol. 34, No. 7)

Offerings Now Encompass Multiplex and Parallel Analysis of Cells, Proteins, and Genes

Affymetrix, best known for its pioneering work in commercializing microarrays for gene expression research since the early 1990s, has grown to become much more than a microarray innovator. Through internal development and acquisitions, it now offers leading-edge technologies for multiplex and parallel analysis of cells, proteins, and genes to advance translational medicine, clinical research, molecular diagnostics, and applied sciences.

“Our portfolio has changed dramatically and now covers the entire spectrum of RNA, DNA, and protein from single-plex to multiplex assays. For example, our ViewRNA™ Assay is an advanced RNA in situ hybridization assay for detection of single transcripts at a single-cell resolution in cell and tissue samples,” says Andy Last, Ph.D., COO.

The company’s 2012 acquisition of eBioscience was pivotal in that transformation. “With eBioscience, we added immunoassays and flow cytometry reagents for protein and cell analysis to our genomics portfolio,” Dr. Last explains. “We now are combining technologies to enable researchers to interrogate a cell in new ways. Our QuantiGene® FlowRNA Assay enables researchers to use RNA probes for flow cytometry in conjunction with traditional flow antibody reagents to interrogate cells in completely new ways.”

In January, the FDA cleared Affymetrix’ CytoScan® Dx Assay. With 2.7 million markers, it is a whole-genome, high-resolution microarray to help diagnose children’s developmental and intellectual disabilities. It can reveal small aberrations not readily seen using traditional techniques. The assay replaces karyotyping, which involves analyzing chromosomes through a microscope and conducting a DNA FISH assay that identifies no more than three markers. The CytoScan assay, in contrast, analyzes the entire genome in a single assay in three days with much higher resolution and improved diagnostic yield.

“The FDA clearance broke new ground,” chief commercial officer David Weber declares. “We’re the first to gain clearance for a molecular diagnostic test for postnatal analysis that analyzes the whole genome in a single assay for DNA copy number changes associated with developmental and intellectual disabilities.”

For CytoScan Dx Assay, the road to commercialization was long. The “for research only” version of the assay, CytoScan Cytogenetics Suite, was launched in 2011 and is sold globally in all major countries. “We worked closely with the FDA through its de novo classification process and obtained the clearance for in vitro diagnostic use,” Weber tells GEN. “Although the underlying molecular biology for the whole-genome assay is complex, the assay is simple to use, incorporating FDA-cleared instruments, a streamlined protocol, and an easy-to-use analysis and reporting software package.”

“Clearance of the CytoScan Dx Assay sets a benchmark for the entire industry,” Dr. Last adds. “Additionally, this positions us as a broad-scale diagnostics player for the future. We also have the Powered by Affymetrix program where we work with our partners, supporting them as they develop their own diagnostics assays on our platform.  This approval paves the way for them to gain clearance and deploy their tests broadly on a cleared and adopted platform.”

The Affymetrix Axiom® genotyping solution provides predesigned and custom arrays.

Genotyping Goes Mainstream

“The medical industry is in high gear around personalized medicine using genetic analysis and companion diagnostics,” Dr. Last says. “By understanding which drugs will or will not be impactful for specific patients, there is immense potential to improve therapy outcomes, avoiding the costs of treatments that may not be effective, and reducing the cost of drug development.”

“The use of genetic analysis is accelerating at a phenomenal pace,” Dr. Last continues. Recently, Affymetrix began working with the U.K. BioBank. The collaborators are using the company’s Axiom® genotyping technology to genotype biological samples from 500,000 individuals. The sample data will be correlated with the participants’ medical records for broad insights into disease onset and progression. It is the largest genotyping study of its kind

Affymetrix is also expanding into the agricultural market with its Axiom genotyping technology for marker-assisted breeding programs. Recent successes include a partnership with the University of Bristol in the U.K. to design an array to genotype wheat as part of the university’s work to ensure sustainable wheat production.

New Company, New Look

In 2013, Affymetrix rebranded the company, launching a new logo and a new look and feel to highlight its transformation from a microarray company to a solutions provider for cell, protein, and genetic analysis in translational research and clinical, molecular diagnostics, and applied markets. “We’re attending different types of conferences now than we did three years ago, such as medical genetics and pathology conferences. We’ve organized our teams around translational medicine, clinical diagnostics, and applied sciences, and we are ensuring our customer interactions are relevant and value-add,” Weber elaborates.

“We sell into very complex scientific areas, so we must stay close to our customers to continue to innovate and meet their scientific needs,” Dr. Last emphasizes. “We have long-standing relationships with leading clinicians and medical institutions. We all share a common goal of rapidly translating the discoveries made in the lab to routine applications in the clinic and in the field,” Dr. Last concludes.


Location: 3420 Central Expressway, Santa Clara, CA 95051
Phone: (408) 731-5000
Principal: Frank Witney, Ph.D., President and CEO
Number of Employees: 1,100
Focus: Affymetrix provides technologies that enable multiplex and parallel analysis of biological systems at the cell, protein, and gene levels, with a particular interest in translational medicine and the clinic research, diagnostics, and applied sciences markets.

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